Newly re-started 3 feet aquarium without CO2 but with controsoil substrate 1 inch and PLL light. Lily sent a stem with leaf on surface of water. Should i cut it or let it remain till it obstructs light to others.

It depends on the type of lily it is. Some make underwater leaves when floating ones are cut off and some do not. It also depends on the lighting and again, the species, if it is too little, the plant will insist on making floaters in search of better light. Dwarf Lily (N nouchali) is very adaptable to low light so it might make underwater leaves again..